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Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor–DNA Interactions with Expression Data: An Entropy-Based Approach

机译:通过整合转录因子-DNA相互作用和表达数据构建基因调控网络的逻辑模型:基于熵的方法

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Abstract Models of gene regulatory networks (GRNs) attempt to explain the complex processes that determine cells' behavior, such as differentiation, metabolism, and the cell cycle. The advent of high-throughput data generation technologies has allowed researchers to fit theoretical models to experimental data on gene-expression profiles. GRNs are often represented using logical models. These models require that real-valued measurements be converted to discrete levels, such as on/off, but the discretization often introduces inconsistencies into the data. Dimitrova et al. posed the problem of efficiently finding a parsimonious resolution of the introduced inconsistencies. We show that reconstruction of a logical GRN that minimizes the errors is NP-complete, so that an efficient exact algorithm for the problem is not likely to exist. We present a probabilistic formulation of the problem that circumvents discretization of expression data. We phrase the problem of error reduction as a minimum entropy problem, ..." /> rel="meta" type="application/atom+xml" href="http://dx.doi.org/10.1089%2Fcmb.2011.0100" /> rel="meta" type="application/rdf+json" href="http://dx.doi.org/10.1089%2Fcmb.2011.0100" /> rel="meta" type="application/unixref+xml" href="http://dx.doi.org/10.1089%2Fcmb.2011.0100" /> 展开▼
机译:摘要基因调控网络(GRN)模型试图解释决定细胞行为的复杂过程,例如分化,代谢和细胞周期。高通量数据生成技术的出现使研究人员能够将理论模型与基因表达谱上的实验数据进行拟合。 GRN通常使用逻辑模型表示。这些模型要求将实值测量值转换为离散级别,例如开/关,但离散化通常会在数据中引入不一致之处。 Dimitrova等。提出了有效地找到所引入的矛盾的简约解决方案的问题。我们表明,将错误最小化的逻辑GRN的重构是NP完全的,因此,不太可能存在针对该问题的有效的精确算法。我们提出了避免表达数据离散化的问题的概率公式。我们将减少错误的问题称为最小熵问题,...“ /> <元名称=”关键字“ content =”算法,计算分子生物学“ /> rel =” meta“ type =” application / atom + xml“ href =” http:// dx .doi.org / 10.1089%2Fcmb.2011.0100“ /> rel =” meta“ type =” application / r df + json“ href =” http://dx.doi.org/10.1089%2Fcmb.2011.0100“ /> rel =” meta“ type =” application / unixref + xml“ href =” http:// dx。 doi.org/10.1089%2Fcmb.2011.0100“ />

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